8WUL: Affinity enhanced TCR

Crystal structure of affinity enhanced TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide (VVGAVGVGK). Determined by X-ray diffraction at 2.36 Å resolution. Released 1 May 2024.

Method: X-ray diffraction
Resolution: 2.36 Å
Organisms: Mus musculus, Homo sapiens
Chains: 20
Atoms: 26,016
Mol. weight: 374.75 kDa
Released: 1 May 2024

Explore 8WUL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WUL contains 79 α-helices and 292 β-strands across 16 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-14	5	12
β-strand	19-25	7	11
β-strand	30-38	9	12
β-strand	45-50	6	12
β-strand	54-58	5	11
β-strand	61-66	6	11
β-strand	71-76	6	11
α-helix	81-83	3
β-strand	85-93	9	12
β-strand	100-101	2	12
β-strand	105-110	6	12
β-strand	119-124	6	13
β-strand	132-137	6	13
β-strand	154-155	2	13
α-helix	156-158	3
β-strand	159-162	4	13
β-strand	169-176	8	13

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	14
β-strand	8-12	5	15
β-strand	17-19	3	16
β-strand	20	1	14
β-strand	22	1	17
β-strand	29-35	7	15
β-strand	42-48	7	15
β-strand	51-55	5	15
β-strand	62-65	4	16
β-strand	71	1	17
β-strand	73-76	4	16
α-helix	81-83	3
β-strand	85-92	8	15
β-strand	103-104	2	15
β-strand	108-113	6	15
α-helix	116-118	3
β-strand	120	1	18
β-strand	123-127	5	19
β-strand	128	1	13
α-helix	129-130	2
α-helix	133-136	4
β-strand	139-149	11	19
β-strand	150	1	18
β-strand	154-160	7	20
β-strand	163-165	3	20
β-strand	169-171	3	19
α-helix	175	1
β-strand	176-179	4	19
β-strand	182-192	11	19
α-helix	193-196	4
β-strand	202-209	8	20
β-strand	212	1	21
β-strand	226	1	21
β-strand	228-235	8	20

Chain C: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-50	6	2
β-strand	54-58	5	1
β-strand	61-66	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	85-91	7	2
β-strand	100-101	2	2
β-strand	105-110	6	2
β-strand	119-124	6	3
β-strand	132-137	6	3
β-strand	154-155	2	3
α-helix	156-158	3
β-strand	159-161	3	3
β-strand	170-176	7	3

Chain D: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	4
β-strand	8-12	5	5
β-strand	17-19	3	6
β-strand	20-23	4	4
β-strand	29-35	7	5
β-strand	42-48	7	5
β-strand	51-55	5	5
β-strand	62-65	4	6
β-strand	71	1	4
β-strand	73-76	4	6
α-helix	81-83	3
β-strand	85-92	8	5
β-strand	103-104	2	5
β-strand	108-113	6	5
α-helix	116-118	3
β-strand	120	1	7
α-helix	121-122	2
β-strand	123-127	5	8
α-helix	128-130	3
α-helix	131-136	6
β-strand	139-149	11	8
β-strand	150	1	7
β-strand	154-160	7	9
β-strand	163-165	3	9
β-strand	169-171	3	8
β-strand	176-179	4	8
β-strand	182-192	11	8
α-helix	193-196	4
β-strand	202-209	8	9
β-strand	212	1	10
β-strand	226	1	10
β-strand	228-235	8	9

Chain E: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-14	5	23
β-strand	19-25	7	22
β-strand	30-38	9	23
β-strand	45-50	6	23
β-strand	54-58	5	22
β-strand	61-66	6	22
β-strand	71-76	6	22
α-helix	81-83	3
β-strand	85-93	9	23
β-strand	100-101	2	23
β-strand	105-110	6	23
β-strand	119-124	6	24
β-strand	132-137	6	24
β-strand	154-155	2	24
β-strand	159-163	5	24
β-strand	168-176	9	24

Chain F: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	25
β-strand	8-12	5	26
β-strand	17-19	3	27
β-strand	20-22	3	25
β-strand	29-35	7	26
β-strand	42-48	7	26
β-strand	51-55	5	26
β-strand	62-65	4	27
β-strand	71	1	25
β-strand	73-76	4	27
α-helix	81-83	3
β-strand	85-92	8	26
β-strand	103-104	2	26
β-strand	108-113	6	26
α-helix	116-118	3
β-strand	120	1	28
β-strand	123-127	5	29
α-helix	128-130	3
α-helix	131-136	6
β-strand	139-149	11	29
β-strand	150	1	28
β-strand	154-160	7	30
β-strand	163-165	3	30
β-strand	169-171	3	29
α-helix	175	1
β-strand	176-179	4	29
β-strand	182-192	11	29
α-helix	193-196	4
β-strand	202-209	8	30
β-strand	212	1	31
β-strand	226	1	31
β-strand	228-235	8	30

Chain G: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	32
β-strand	10-14	5	33
β-strand	19-24	6	32
β-strand	33-38	6	33
β-strand	45-50	6	33
β-strand	54-58	5	32
β-strand	61-66	6	32
β-strand	71-76	6	32
α-helix	81-83	3
β-strand	85-91	7	33
β-strand	100-101	2	33
β-strand	105-110	6	33
β-strand	119-124	6	34
β-strand	132-137	6	34
β-strand	151	1	35
β-strand	153	1	35
β-strand	154-155	2	34
α-helix	156-158	3
β-strand	159-161	3	34
β-strand	170-176	7	34

Chain H: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	36
β-strand	8-12	5	37
β-strand	17-19	3	38
β-strand	20-22	3	36
β-strand	29-35	7	37
β-strand	42-48	7	37
β-strand	51-55	5	37
β-strand	62-65	4	38
β-strand	71	1	36
β-strand	73-76	4	38
α-helix	81-83	3
β-strand	85-92	8	37
β-strand	103-104	2	37
β-strand	108-113	6	37
α-helix	116-118	3
β-strand	120	1	39
β-strand	123-127	5	40
β-strand	128	1	34
α-helix	129-130	2
α-helix	131-136	6
β-strand	139-149	11	40
β-strand	150	1	39
β-strand	154-160	7	41
β-strand	163-165	3	41
β-strand	169-171	3	40
β-strand	176-179	4	40
β-strand	182-192	11	40
α-helix	193-196	4
β-strand	202-209	8	41
β-strand	212	1	42
β-strand	226	1	42
β-strand	228-235	8	41

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR alpha chain	A, C, E, G	protein	198	Mus musculus	P01849 (AlphaFold model), Q5R1I3 (AlphaFold model)
TCR beta chain	B, D, F, H	protein	239	Mus musculus
MHC class I antigen	I, L, O, R	protein	274	Homo sapiens	A0A583ZB34 (AlphaFold model)
Beta-2-microglobulin	J, M, P, S	protein	99	Homo sapiens	P61769 (AlphaFold model)
KRAS-G12V nonamer peptide	K, N, Q, T	protein	9	Homo sapiens	P01116

Sequence of entity 1 (A, C, E, G), FASTA

>8WUL_1 TCR alpha chain (chains A, C, E, G)
QQKVQQSPESLIVPEGGMASLNCTSSDRNVDYFWWYRQHSGKSPKMLMSIFSNGEKEEGR
FTVHLNKASLHTSLHIRDSQPSDSALYLCAARSSGSWQLIFGSGTQLTVMPDIQNPEPAV
YQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGAIAWSNQT
SFTCQDIFKETNATYPSS

Sequence of entity 2 (B, D, F, H), FASTA

>8WUL_2 TCR beta chain (chains B, D, F, H)
KIIQKPKYLVAVTGSEKILICEQYLGHNAMYWYRQSAKKPLEFMFSYSYQMLMDNQTASS
RFQPQSSKKNHLDLQITALKPDDSATYFCASSQDRGDSAHTLYFGSGTRLTVLEDLRNVT
PPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESN
YSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD

Sequence of entity 3 (I, L, O, R), FASTA

>8WUL_3 MHC class I antigen (chains I, L, O, R)
GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 4 (J, M, P, S), FASTA

>8WUL_4 Beta-2-microglobulin (chains J, M, P, S)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (K, N, Q, T), FASTA

>8WUL_5 KRAS-G12V nonamer peptide (chains K, N, Q, T)
VVGAVGVGK

Primary citation

Identification and affinity enhancement of T-cell receptor targeting a KRAS G12V cancer neoantigen. Zhang, M., Xu, W., Luo, L. et al. Commun Biol (2024) 7:512-512. DOI 10.1038/s42003-024-06209-2 · PubMed

Other PDB entries of the same protein (UniProt P01849 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
2Q86 1.85 Å, Structure of the mouse invariant NKT cell receptor Valpha14
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…
1LP9 2.0 Å, Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1
8WTE 2.17 Å, Crystal structure of TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide…
2JCC 2.5 Å, AH3 recognition of mutant HLA-A2 W167A
1NFD 2.8 Å, An alpha-beta T cell receptor (TCR) heterodimer in complex with an anti-TCR FAB fragment…
2J8U 2.88 Å, Large CDR3a loop alteration as a function of MHC mutation.
3MBE 2.89 Å, TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
3C6L 3.4 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20
6MF8 TCR alpha transmembrane domain

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